Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Padua, Italy.
Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
PLoS One. 2018 Jun 29;13(6):e0199950. doi: 10.1371/journal.pone.0199950. eCollection 2018.
Members of the genus Circovirus are host-specific viruses, which are totally dependent on cell machinery for their replication. Consequently, certain mimicry of the host genome features is expected to maximize cellular replicative system exploitation and minimize the recognition by the innate immune system. In the present study, the analysis of several genome composition and codon bias parameters of circoviruses infecting avian and mammalian species demonstrated the presence of quite distinctive patterns between the two groups. Remarkably, a higher deviation from the expected values based only on mutational patterns was observed for mammalian circoviruses both at dinucleotide and codon levels. Accordingly, a stronger selective pressure was estimated to shape the genome of mammalian circoviruses, particularly in the Cap encoding gene, compared to avian circoviruses. These differences could be attributed to different physiological and immunological features of the two host classes and suggest a trade-off between a tendency to optimize the capsid protein translation while minimizing the recognition of the genome and the transcript molecules. Interestingly, the recently identified Porcine circovirus 3 (PCV-3) had an intermediate pattern in terms of genome composition and codon bias. Particularly, its Rep gene appeared closely related to other mammalian circoviruses (especially bat circoviruses) while the Cap gene more closely resembled avian circoviruses. These evidences, coupled with the high selective forces apparently modelling the PCV-3 Cap gene composition, suggest the potential recombinant origin, followed or preceded by a host jump, of this virus.
圆环病毒属的成员是宿主特异性病毒，完全依赖于细胞机制进行复制。因此，预计某些对宿主基因组特征的模拟将最大限度地利用细胞复制系统，并最大限度地减少先天免疫系统的识别。在本研究中，对感染禽类和哺乳动物的圆环病毒的几种基因组组成和密码子偏好参数的分析表明，这两组之间存在相当明显的模式。值得注意的是，无论是在二核苷酸还是密码子水平上，哺乳动物圆环病毒的偏离预期值的程度都比禽类圆环病毒更高。因此，与禽类圆环病毒相比，估计有更强的选择压力来塑造哺乳动物圆环病毒的基因组，特别是在 Cap 编码基因中。这些差异可能归因于两种宿主类别的不同生理和免疫特征，并表明在优化衣壳蛋白翻译的倾向与最小化基因组和转录本分子的识别之间存在权衡。有趣的是，最近发现的猪圆环病毒 3（PCV-3）在基因组组成和密码子偏好方面呈现出中间模式。特别是，其 Rep 基因与其他哺乳动物圆环病毒（特别是蝙蝠圆环病毒）密切相关，而 Cap 基因更类似于禽类圆环病毒。这些证据，加上明显塑造 PCV-3 Cap 基因组成的高选择压力，表明该病毒可能是通过重组产生的，随后或之前发生了宿主跳跃。
